Förster Resonance Energy Transfer in Linear DNA Multifluorophore Photonic Wires: Comparing Dual versus Split Rail Building Block Designs

Abstract

DNA scaffolds provide a means to precisely organize chromophores into large biomimetic exciton networks and direct energy transport for nanoscale sensing and light‐harvesting applications. Here, a functional building block of minimal complexity that maximizes the Förster resonance energy transfer (FRET) efficiency is sought. Using a model system consisting of three FRET steps in a 4‐dye cascade: Cy3→Cy3.5→Cy5→Cy5.5, we evaluate how this building block employs multiple interacting versus redundant FRET pathways. Variants of a dual rail design, where one or two copies of each dye are aligned in rigid linear parallel rows, are compared to a split rail format, where varying degrees of spacing are introduced between the rows. The FRET processes are assessed via steady‐state, time‐resolved, and single‐molecule spectroscopy. Experiments and simulation reveal the dual rail design as more efficient than the split rail and suggest the design principle that efficient FRET networks must balance the increase in FRET rate from multiple interacting pathways with undesirable fluorescence quenching between dyes in close proximity. Hybrid fluorophore combinations are identified as a strategy to mitigate this quenching, leading to optimized dual rails capable of 50% end‐to‐end efficiency. These insights can help guide the design of functional photonic wires based on DNA scaffolds.

Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis

“…In terms of ET, various D–A cyanine dyes displaying a range of absorption and emission maxima have been used to label oligonucleotides that are then assembled into designer DNA structures allowing them to function as so-called molecular photonic wires . Within these structures, a variety of parameters can be iteratively modified and tested either jointly or independently including that of D/A ratios, D/A spacing, number of ET steps, relative dye orientation, interactions with other dyes, structural dimensionality (planar vs 3D), dye density, and so forth. − Cumulatively, this provides a powerful system to develop design strategies to optimally harvest light and then focus it on the nanoscale. To exploit exciton delocalization, DNA structures such as Holliday junctions allow the cyanine dyes to strongly interact and provide access to intriguing optical phenomena such as displaying J- and H-aggregate behavior along with large Davydov splitting. − Harnessing such exciton delocalization properties, especially at room temperature, is of interest for the development of new types of hyperefficient light harvesters and sensors along with excitonic devices that exploit coherence for quantum information processing.…”

“…The inherent modularity of DNA assembly also allows experimental structures and the necessary controls to be easily assembled in a parallel side-by-side format. Indeed, reflecting the power of DNA nanotechnology’s inherently parallel reaction assembly chemistry, some reports have assembled hundreds of different targets and control structures in total to provide necessary data on all potentially contributing ET processes by making almost every possible combination. − Several cyanine dye analogues are available through commercial sources which display reactive functional groups that enable dye incorporation both during and post DNA synthesis, for example, phosphoramidite and N -hydroxy­succinimidyl ester/maleimide derivatives, respectively. − Due to the chemical nature of these functional groups, longer attachment linkers are also often required, which can allow significant conformational freedom of individual dyes within DNA constructs. Excessive freedom of movement can be detrimental to excitonic coupling applications on DNA scaffolds due to positional uncertainty and lack of control over orientation and dye-to-dye interactions.…”

Engineering Exciton Dynamics with Synthetic DNA Scaffolds

“…Toward the objective of building a blueprint for effective energy and charge carrier transduction, the scalability of DNA origami with chromophore modifications to only the staple strands presents the opportunity to move beyond one-dimensional structures. , This would enable energy-transfer characteristics to be established according to dimensionality, Euclidean geometry, and varying extents of structural and energetic disorder. Applications of conversion and sensing with millisecond time scale dynamics can also be accessed by incorporating toeholds and strand displacement schemes that can modulate DNA architectures accordingly.…”

“…The rigidity and stability of these branched motifs can be greatly enhanced using four-way double-crossover (DX) tiles, where the branch point is built from two duplexes and up to four strands. We and others , have deployed this motif to assemble noncovalent aggregates, where the beneficial rigidity of the two closely spaced duplexes provides a longer persistence length for the active A-T-rich neighboring duplex. Importantly, the DX tile is also the principle component of DNA origami, a technology that uses long multikilobase ssDNA as a scaffold for large (100 nm to 10 μm) structures that can support extend multichromophore assemblies in complex geometries, on the order of natural light-harvesting systems. ,, …”

Highly Emissive Organic Cage in Single-Molecule and Aggregate States by Anchoring Multiple Aggregation-Caused Quenching Dyes

“…Thus far, there are two pathways to construct this kind of molecule: one strategy is to lock AIE chromophore units within cages or networks, resulting in emissive materials by reducing phenyl rotation, but such a kind of AIE molecule is limited. The other strategy is using ACQ molecules as building blocks by incorporating bulky substituents into their scaffolds to avoid strong π–π stacking − or arranging the ACQ molecules with the help of templates, such as organic–inorganic hybrid materials, , dendritic polymers, − micelles, − organogels, − and biomaterials, − to avoid the self-quenching. However, it remains difficult to satisfy both the high local density and symmetrical distribution of chromophores with a high fluorescence quantum yield and high stability as well as good biocompatibility.…”